1TX9 | pdb_00001tx9

gpd prior to capsid assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 
    0.310 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.271 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.280 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Conformational switching by the scaffolding protein D directs the assembly of bacteriophage phiX174

Morais, M.C.Fisher, M.Kanamaru, S.Przybyla, L.Burgner, J.Fane, B.A.Rossmann, M.G.

(2004) Mol Cell 15: 991-997

  • DOI: https://doi.org/10.1016/j.molcel.2004.08.023
  • Primary Citation Related Structures: 
    1TX9

  • PubMed Abstract: 

    The three-dimensional structure of bacteriophage phiX174 external scaffolding protein D, prior to its interaction with other structural proteins, has been determined to 3.3 angstroms by X-ray crystallography. The crystals belong to space group P4(1)2(1)2 with a dimer in the asymmetric unit that closely resembles asymmetric dimers observed in the phiX174 procapsid structure. Furthermore, application of the crystallographic 4(1) symmetry operation to one of these dimers generates a tetramer similar to the tetramer in the icosahedral asymmetric unit of the procapsid. These data suggest that both dimers and tetramers of the D protein are true morphogenetic intermediates and can form independently of other proteins involved in procapsid morphogenesis. The crystal structure of the D scaffolding protein thus represents the state of the polypeptide prior to procapsid assembly. Hence, comparison with the procapsid structure provides a rare opportunity to follow the conformational switching events necessary for the construction of complex macromolecular assemblies.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA.

Macromolecule Content 

  • Total Structure Weight: 33.64 kDa 
  • Atom Count: 2,125 
  • Modeled Residue Count: 271 
  • Deposited Residue Count: 302 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Scaffolding protein D
A, B
151Sinsheimervirus phiX174Mutation(s): 0 
Gene Names: D
UniProt
Find proteins for P69486 (Enterobacteria phage phiX174)
Explore P69486 
Go to UniProtKB:  P69486
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69486
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free:  0.310 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.271 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.280 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.44α = 90
b = 106.44β = 90
c = 127.019γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Refinement description